You don't. Cafiine was created to mod retail games.
To mod a game running within Loadiine GX2, all you need to do is put the mod files on your SD Card on top of the original files (the game's files are in sd:/wiiu/games/Game Name [GAMEID]/content) - though Cafiine mods should work with this principle.
You can also put your mods into an 'updates' folder which gives you the ability to enable/disable your mod within Loadiine. See the Loadiine thread for exact details, as I don;t remember what those details are.